Nucleic acids from stool samples that are analyzed for the presence of mutations and/or for methylation status associated with disease or risk of disease typically pass through a number of process steps during analysis. These steps may comprise, e.g., filtration, precipitation, capture, washing, elution, and/or chemical modification. For analysis of DNAs to determine methylation status, processing typically comprises treatment with bisulfite to covert unmethylated dC bases to dU residues, making them more readily distinguishable from the methyl-C residues that are protected from bisulfite conversion.
Sample processing steps can be evaluated for efficiency and efficacy by the use of control DNAs of known composition. For mutation detection assays, plasmid DNAs containing cloned DNA fragments containing wild type and mutant sequences may be used, for example. For analysis of methylation of control DNAs, however, plasmid DNA cannot be used as the bacterial host cells typically used to grow plasmids do not methylate C residues in the same manner as would be found in mammalian cells. Treatment of DNA after isolation, e.g., with a DNA methylase, also cannot reliably reproduce DNA having a degree and pattern of methylation accurately reflecting actual target DNA. Thus, there is a need for synthetic nucleic acid compositions that can act as accurate controls for stool-derived target DNAs through all of the steps of processing and detection.